Watching plants grow:A position paper on computer vision and Arabidopsis thaliana

The authors present a comprehensive overview of image processing and analysis work done to support research into the model flowering plant Arabidopsis thaliana. Beside the plant's importance in biological research, using image analysis to obtain experimental measurements of it is an interesting vision problem in its own right, involving the segmentation and analysis of sequences of images of objects whose shape varies between individual specimens and also changes over time. While useful measurements can be obtained by segmenting a whole plant from the background, they suggest that the increased range and precision of measurements made available by leaf‐level segmentation makes this a problem well worth solving. A variety of approaches have been tried by biologists as well as computer vision researchers. This is an interdisciplinary area and the computer vision community has an important contribution to make. They suggest that there is a need for publicly available datasets with ground truth annotations to enable the evaluation of new approaches and to support the building of training data for modern data‐driven computer vision approaches, which are those most likely to result in the kind of fully automated systems that will be of use to biologists

Aerosol chemical composition at Cabouw, The Netherlands as observed in two intensive periods in May 2008 and March 2009

Observations of aerosol chemical composition in Cabauw, the Netherlands, are presented for two intensive measurement periods in May 2008 and March 2009. Sub-micron aerosol chemical composition was measured by an Aerodyne Aerosol Mass Spectrometer (AMS) and is compared to observations from aerosol size distribution measurements as well as composition measurements with a Monitor for AeRosol and GAses (MARGA) based instrument and a Thermal-Desorption Proton-Transfer-Reaction Mass-Spectrometer (TD-PTR-MS). An overview of the data is presented and the data quality is discussed. In May 2008 enhanced pollution was observed with organics contributing 40% to the PM1 mass. In contrast the observed average mass loading was lower in March 2009 and a dominance of ammonium nitrate (42%) was observed. The semi-volatile nature of ammonium nitrate is evident in the diurnal cycles with maximum concentrations observed in the morning hours in May 2008 and little diurnal variation observed in March 2009. Size dependent composition data from AMS measurements are presented and show a dominance of organics in the size range below 200 nm. A higher O:C ratio of the organics is observed for May 2008 than for March 2009. Together with the time series of individual tracer ions this shows the dominance of OOA over HOA in May 2008

The formation, properties and impact of secondary organic aerosol: current and emerging issues

Secondary organic aerosol (SOA) accounts for a significant fraction of ambient tropospheric aerosol and a detailed knowledge of the formation, properties and transformation of SOA is therefore required to evaluate its impact on atmospheric processes, climate and human health. The chemical and physical processes associated with SOA formation are complex and varied, and, despite considerable progress in recent years, a quantitative and predictive understanding of SOA formation does not exist and therefore represents a major research challenge in atmospheric science. This review begins with an update on the current state of knowledge on the global SOA budget and is followed by an overview of the atmospheric degradation mechanisms for SOA precursors, gas-particle partitioning theory and the analytical techniques used to determine the chemical composition of SOA. A survey of recent laboratory, field and modeling studies is also presented. The following topical and emerging issues are highlighted and discussed in detail: molecular characterization of biogenic SOA constituents, condensed phase reactions and oligomerization, the interaction of atmospheric organic components with sulfuric acid, the chemical and photochemical processing of organics in the atmospheric aqueous phase, aerosol formation from real plant emissions, interaction of atmospheric organic components with water, thermodynamics and mixtures in atmospheric models. Finally, the major challenges ahead in laboratory, field and modeling studies of SOA are discussed and recommendations for future research directions are proposed

Organic nitrate and secondary organic aerosol yield from NO3 oxidation of ß-pinene evaluated using a gas-phase kinetics/aerosol partitioning model

The yields of organic nitrates and of secondary organic aerosol (SOA) particle formation were measured for the reaction NO3+beta-pinene under dry and humid conditions in the atmosphere simulation chamber SAPHIR at Research Center Julich. These experiments were conducted at low concentrations of NO3 (NO3+N2O5 < 10 ppb) and beta-pinene (peak similar to 15 ppb), with no seed aerosol. SOA formation was observed to be prompt and substantial (similar to 50% mass yield under both dry conditions and at 60% RH), and highly correlated with organic nitrate formation. The observed gas/aerosol partitioning of organic nitrates can be simulated using an absorptive partitioning model to derive an estimated vapor pressure of the condensing nitrate species of p(vap) similar to 5x10(-6) Torr (6.67x10(-4) Pa), which constrains speculation about the oxidation mechanism and chemical identity of the organic nitrate. Once formed the SOA in this system continues to evolve, resulting in measurable aerosol volume decrease with time. The observations of high aerosol yield from NOx-dependent oxidation of monoterpenes provide an example of a significant anthropogenic source of SOA from biogenic hydrocarbon precursors. Estimates of the NO3+beta-pinene SOA source strength for California and the globe indicate that NO3 reactions with monoterpenes are likely an important source (0.5-8% of the global total) of organic aerosol on regional and global scales

Evolution of the complex refractive index in the UV spectral region in ageing secondary organic aerosol

The chemical and physical properties of secondary organic aerosol (SOA) formed by the photochemical degradation of biogenic and anthropogenic volatile organic compounds (VOC) are as yet still poorly constrained. The evolution of the complex refractive index (RI) of SOA, formed from purely biogenic VOC and mixtures of biogenic and anthropogenic VOC, was studied over a diurnal cycle in the SAPHIR photochemical outdoor chamber in Jülich, Germany. The correlation of RI with SOA chemical and physical properties such as oxidation level and volatility was examined. The RI was retrieved by a newly developed broadband cavity-enhanced spectrometer for aerosol optical extinction measurements in the UV spectral region (360 to 420 nm). Chemical composition and volatility of the particles were monitored by a high-resolution time-of-flight aerosol mass spectrometer, and a volatility tandem differential mobility analyzer. SOA was formed by ozonolysis of either (i) a mixture of biogenic VOC (α-pinene and limonene), (ii) biogenic VOC mixture with subsequent addition of an anthropogenic VOC (<i>p</i>-xylene-d₁₀), or (iii) a mixture of biogenic and anthropogenic VOC. The SOA aged by ozone/OH reactions up to 29.5 h was found to be non-absorbing in all cases. The SOA with <i>p</i>-xylene-d₁₀ showed an increase of the scattering component of the RI correlated with an increase of the O / C ratio and with an increase in the SOA density. There was a greater increase in the scattering component of the RI when the SOA was produced from the mixture of biogenic VOCs and anthropogenic VOC than from the sequential addition of the VOCs after approximately the same ageing time. The increase of the scattering component was inversely correlated with the SOA volatility. Two RI retrievals determined for the pure biogenic SOA showed a constant RI for up to 5 h of ageing. Mass spectral characterization shows the three types of the SOA formed in this study have a significant amount of semivolatile components. The influence of anthropogenic VOCs on the oxygenated organic aerosol as well as the atmospheric implications are discussed

Towards an online-coupled chemistry-climate model: evaluation of trace gases and aerosols in COSMO-ART

Peer reviewe

Enhancement of the aerosol direct radiative effect by semi-volatile aerosol components: airborne measurements in North-Western Europe

A case study of atmospheric aerosol measurements exploring the impact of the vertical distribution of aerosol chemical composition upon the radiative budget in North-Western Europe is presented. Sub-micron aerosol chemical composition was measured by an Aerodyne Aerosol Mass Spectrometer (AMS) on both an airborne platform and a ground-based site at Cabauw in the Netherlands. The examined period in May 2008 was characterised by enhanced pollution loadings in North-Western Europe and was dominated by ammonium nitrate and Organic Matter (OM). Both ammonium nitrate and OM were observed to increase with altitude in the atmospheric boundary layer. This is primarily attributed to partitioning of semi-volatile gas phase species to the particle phase at reduced temperature and enhanced relative humidity. Increased ammonium nitrate concentrations in particular were found to strongly increase the ambient scattering potential of the aerosol burden, which was a consequence of the large amount of associated water as well as the enhanced mass. During particularly polluted conditions, increases in aerosol optical depth of 50–100% were estimated to occur due to the observed increase in secondary aerosol mass and associated water uptake. Furthermore, the single scattering albedo was also shown to increase with height in the boundary layer. These enhancements combined to increase the negative direct aerosol radiative forcing by close to a factor of two at the median percentile level. Such increases have major ramifications for regional climate predictions as semi-volatile components are often not included in aerosol models. The results presented here provide an ideal opportunity to test regional and global representations of both the aerosol vertical distribution and subsequent impacts in North-Western Europe. North-Western Europe can be viewed as an analogue for the possible future air quality over other polluted regions of the Northern Hemisphere, where substantial reductions in sulphur dioxide emissions have yet to occur. Anticipated reductions in sulphur dioxide in polluted regions will result in an increase in the availability of ammonia to form ammonium nitrate as opposed to ammonium sulphate. This will be most important where intensive agricultural practises occur. Our observations over North-Western Europe, a region where sulphur dioxide emissions have already been reduced, indicate that failure to include the semi-volatile behaviour of ammonium nitrate will result in significant errors in predicted aerosol direct radiative forcing. Such errors will be particularly significant on regional scales